Fig. 6: Reduction of pregnancy gene expression is associated with loss of chromatin accessibility at intronic LTR elements.
a, Genome browser screenshot of the PSG gene cluster in the STs from the snRNA-seq and bulk RNA-seq. The purple shading highlights LTR8B elements within each PSG gene. The pseudo-bulk tracks from the snRNA-seq and bulk RNA-seq tracks are displayed as RPM with y axes ranging from 0 to 300 and 0 to 100, respectively. b, Average expression levels, calculated by Seurat, of the PSG1 (top), PSG4 (middle) and PSG9 genes (bottom) in trophoblast cell types from the snRNA-seq in patient and control samples. c, Expression levels, determined using RT–qPCR, of eight PSG genes in patient and control samples. Expression was normalized to TBP. Each dot represents a sample (n = 7 for both patient and control); P values were calculated using a one-tailed Wilcoxon test. The centre and bounds of boxes indicate the median and quartile of all data points, respectively. The minima and maxima of whiskers indicate quartile 1 − 1.5× the interquartile range and quartile 3 + 1.5× the interquartile range, respectively. d, Immunohistochemistry staining (left) and H scores (right) of PSG9 protein in patient and control samples. Red arrowheads indicate STs and green arrowheads indicate cytotrophoblasts. Scale bars, 50 µm. Each dot in the bar chart represents a sample (n = 7 for patient and n = 6 for control). Data are presented as the mean values with error bars showing the s.e.m.; P values were calculated using a two-tailed Student’s t-test. e, Genome browser screenshot showing the PSG4 gene and its intronic LTR8B element, highlighted by the blue shading. The pseudo-bulk tracks from the snRNA-seq and snATAC-seq are displayed as RPM. The H3K27ac CUT&Tag tracks are displayed as aggregated RPM. The y axes range from 0 to 60 for the snRNA-seq, 0 to 4 for the snATAC-seq and 0 to 2 for the CUT&Tag. Ctrl, control and Cov, COVID-19; cell-type abbreviations as per Fig. 1b.
